Exam 2 Study Guide - Protein Function

Question 1

What is a heme?

Answer 1

protein-bound prosthetic group (present in myoglobin and hemoglobin)

Question 2

What is the structure of heme?

Answer 2

complex organic ring structure, protoporphyrin, with a bound Fe (2+) atom

Question 3

Describe the binding of Fe to the heme and globin molecules.

Answer 3

• Fe bind to heme via 6 bonds (4 to nitrogen atoms in the porphyrin ring and 2 perpendicular to the porphyrin)
• Perpendicular bonds: one is occupied by proximal His residue and one is the binding site for molecular oxygen…Fe (2+) binds O2 reversibly…Fe (3+) does not bind O2

Question 4

What is Ka – the association constant?

Answer 4

Provides a measure of the affinity of the ligand L for the protein (higher Ka, higher affinity)

Question 5

Define “Y” and understand the relationship between Y and L.

Answer 5

The amount of ligand present is proportional to the ratio between bound ligand and free protein (hyperbolic function)

Question 6

What is Kd – the dissociation constant.

Answer 6

Reciprocal of Ka (lower Kd, higher affinity)

Question 7

Proteins A and B both bind ligand L. Which one has the higher affinity for the ligand?

Answer 7

Protein A has the higher affinity for the ligand because Kd is lower at ½ of the available ligand, resulting in a higher affinity

Question 8

Explain how myoglobin increases the binding affinity of Fe for oxygen.

Answer 8

Myoglobin binding to heme causes the affinity for O2 to increase; distal His rotates to open and close the pocket

Question 9

Describe how the binding of oxygen changes the three-dimensional structure of hemoglobin.

Answer 9

Hydrogen bond between the side chain of His E7 and bound O2 electrostatically stabilizes the Fe-O2 polar complex (20,000-fold stronger binding affinity of free heme for CO compared with O2 declines to 40-fold)

Question 10

Describe the composition of muscle proteins.

Answer 10

Composed of actin (thin) and myosin (thick) protein; filaments that interact and slide past each other to bring about contraction

Question 11

Describe how actin and myosin interact to facilitate muscle contraction.

Answer 11

The myosin thick filaments and actin thin filaments are sliding past one another, making the muscles contract/stiffen as rigor mortis sets in. To be more specific, there are 4 steps involved in the molecular mechanism of muscle contraction. First, ATP binds to the myosin head, causing myosin to dissociate from actin. Then, the bound ATP is hydrolyzed and a conformational change in myosin occurs (ADP + P are still attached to myosin). Third, myosin heads attach to actin filaments, causing release of phosphorus…attachment occurs upstream of where it was previously attached. Lastly, the release of P triggers a “power stroke” conformational change in myosin, causing it to slide against actin filament (ADP is released).

Question 12

What is hemoglobin?

Answer 12

responsible for O2 transportation in the bloodstream

Question 13

What is myoglobin?

Answer 13

facilitates O2 diffusion in muscle tissue

Question 14

Which part of the hemoglobin molecule binds to oxygen:

Answer 14

Heme

Question 15

How many bonds can the iron in hemoglobin make?

Answer 15

6

Question 16

Describe the tertiary structure of myoglobin.

Answer 16

Tertiary structure of myoglobin consists of 8 alpha helices. The structure of myoglobin is highly conserved and its folding pattern, constitutes a structural motif known as the globin fold.

Question 17

The structure of myoglobin is highly conserved among different organisms. Why do you think that is?

Answer 17

Myoglobin’s structure has been highly conserved among different organisms because it is essential for life as it facilitates O2 diffusion in muscle tissue. The function of myoglobin depends on the proteins ability to bind oxygen and release it when and where it’s needed; therefore the structure is highly conserved so it can provide these essential functions to numerous organisms.

Question 18

Protein A has a Kd of 3.0 x 10-7 M for ligand X. Protein B has a Kd of 4.0 x 10-8 M for ligand X. Which of these two proteins has a higher affinity for ligand X? How do you know?

Answer 18

Protein B has a high affinity for ligand X because it’s Kd is smaller, indicating protein B will be half saturated at a lower concentration of X than protein A. I know this because the lower value of Kd corresponds to a higher affinity of ligand. With more tight binding within a protein binding to ligand, the lower the concentration of ligand required for half the binding sites to be occupies, and in turn a lower value of Kd will be observed.

Question 19

Explain how calcium binding to troponin controls muscle contraction.

Answer 19

Causes a conformational change in myosin (troponin units on actin myofilaments are bound by calcium ions…. calcium binding displaces tropomyosin along the myofilaments, and in-turn exposes myosin-binding sites)